Evaluation of the contribution of environmental factors

For the simulated data of GAW11, the roles of two environmental factors, E1 and E2, were investigated. Logistic regression analyses measuring the association between outcome (either mild or severe disease versus no disease) and E1 and E2 exposure indicated that E1 was a risk factor for disease (either mild or severe) but that E2 was not associated with outcome. Linkage analyses were performed for strata defined by E1 and E2 exposure. A specific disease locus was identified in these stratified analyses where this locus would not have been identified with an unstratified linkage analysis. Finally, stratified generalized transmission disequilibrium test analyses yielded several false positive results.